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commit: 185edf7edae700779fb362e1adba1042514420da |
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Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> |
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AuthorDate: Mon Feb 1 04:36:18 2021 +0000 |
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Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> |
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CommitDate: Mon Feb 1 04:36:18 2021 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=185edf7e |
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|
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sci-biology/ncbi-blast+: drop py2 only versions |
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|
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Package-Manager: Portage-3.0.14, Repoman-3.0.2 |
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Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> |
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|
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sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild | 352 --------------------- |
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sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild | 355 --------------------- |
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sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild | 360 ---------------------- |
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sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild | 2 +- |
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4 files changed, 1 insertion(+), 1068 deletions(-) |
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|
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diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild |
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deleted file mode 100644 |
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index 05c844b1c..000000000 |
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--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild |
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+++ /dev/null |
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@@ -1,352 +0,0 @@ |
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-# Copyright 1999-2021 Gentoo Authors |
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-# Distributed under the terms of the GNU General Public License v2 |
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- |
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-EAPI=7 |
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- |
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-PYTHON_COMPAT=( python2_7 ) |
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- |
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-inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs |
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- |
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-MY_P="ncbi-blast-${PV}+-src" |
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-# workdir/ncbi-blast-2.2.30+-src |
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-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz |
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- |
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-DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+" |
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-HOMEPAGE="https://ncbi.github.io/cxx-toolkit/" |
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-SRC_URI=" |
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- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz" |
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-# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" |
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- |
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-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz |
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-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html |
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-LICENSE="public-domain" |
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-SLOT="0" |
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-IUSE=" |
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- debug static-libs static threads pch |
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- test wxwidgets odbc |
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- berkdb boost bzip2 cppunit curl expat fltk freetype gif |
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- glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python |
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- sablotron sqlite tiff xerces xalan xml xpm xslt X" |
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-KEYWORDS="~amd64 ~x86" |
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-RESTRICT="!test? ( test )" |
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- |
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-REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
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- |
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-# sys-libs/db should be compiled with USE=cxx |
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-DEPEND=" |
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- <sys-devel/gcc-10:= |
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- !sci-biology/ncbi-tools++ |
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- !sci-biology/sra_sdk |
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- berkdb? ( sys-libs/db:4.3[cxx] ) |
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- boost? ( dev-libs/boost ) |
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- curl? ( net-misc/curl ) |
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- sqlite? ( dev-db/sqlite:3 ) |
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- mysql? ( virtual/mysql ) |
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- fltk? ( x11-libs/fltk ) |
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- opengl? ( virtual/opengl media-libs/glew:0= ) |
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- mesa? ( media-libs/mesa[osmesa] ) |
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- glut? ( media-libs/freeglut ) |
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- freetype? ( media-libs/freetype ) |
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- gnutls? ( net-libs/gnutls ) |
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- python? ( ${PYTHON_DEPS} ) |
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- cppunit? ( dev-util/cppunit ) |
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- icu? ( dev-libs/icu ) |
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- expat? ( dev-libs/expat ) |
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- sablotron? ( app-text/sablotron ) |
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- xml? ( dev-libs/libxml2 ) |
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- xslt? ( dev-libs/libxslt ) |
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- xerces? ( dev-libs/xerces-c ) |
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- xalan? ( dev-libs/xalan-c ) |
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- muparser? ( dev-cpp/muParser ) |
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- hdf5? ( sci-libs/hdf5[cxx] ) |
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- gif? ( media-libs/giflib ) |
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- jpeg? ( virtual/jpeg:0= ) |
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- png? ( media-libs/libpng:0= ) |
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- tiff? ( media-libs/tiff:0= ) |
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- xpm? ( x11-libs/libXpm ) |
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- dev-libs/lzo |
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- app-arch/bzip2 |
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- dev-libs/libpcre" |
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-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge |
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-# Intentionally omitted USE flags: |
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-# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. |
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-# The default (heavily patched) embedded copy should work, or you can |
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-# leave it off altogether -- the only public apps that make use of it are |
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-# samples and tests, since NCBI's database servers are of course firewalled. |
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- |
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-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) |
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- |
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-RDEPEND="${DEPEND}" |
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- |
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-S="${WORKDIR}/${MY_P}/c++" |
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-# ncbi-blast-2.2.30+-src/c++ |
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- |
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-src_prepare() { |
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-# filter-ldflags -Wl,--as-needed |
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-# append-ldflags -Wl,--no-undefined |
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-# sed -i -e 's/-print-file-name=libstdc++.a//' \ |
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-# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ |
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-# src/build-system/configure || die |
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-# epatch \ |
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-# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ |
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-# "${FILESDIR}"/curl-types.patch \ |
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-# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ |
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-# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ |
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-# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ |
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-# "${FILESDIR}"/report_project_settings_configure.ac.patch \ |
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-# "${FILESDIR}"/report_project_settings_configure.patch \ |
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-# "${FILESDIR}"/make_install.patch |
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- |
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-# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch |
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- |
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-# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ |
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-# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ |
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-# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ |
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-# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ |
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-# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch |
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- |
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-# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" |
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- |
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-# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers |
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-## local PATCHES=( |
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-## "${FILESDIR}"/${P}-conf-opts.patch |
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-## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch |
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-## "${FILESDIR}"/${P}-linkage-tuneups.patch |
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-## "${FILESDIR}"/${P}-more-patches.patch |
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-## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch |
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-## "${FILESDIR}"/${P}-configure.patch |
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-## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch |
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-## "${FILESDIR}"/${P}-fix-install.patch |
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-## ) |
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- # "${FILESDIR}"/${P}-support-autoconf-2.60.patch |
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-## epatch ${PATCHES[@]} |
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- |
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- # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup |
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- epatch "${FILESDIR}"/"${P}"__fix_lib_deps.patch |
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- # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 |
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- # https://bugs.gentoo.org/show_bug.cgi?id=514706 |
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- |
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- tc-export CXX CC |
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- |
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-## cd src/build-system || die |
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-# eautoreconf |
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- |
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- # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch |
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- # eautoconf # keep it disabled until we can ensure 2.59 is installed |
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- # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support |
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- default |
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-} |
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- |
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-# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site |
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-src_configure() { |
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- local myconf=() |
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- #--without-optimization turn off optimization flags in non-debug mode |
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- #--with-profiling build profiled versions of libs and apps |
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- #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) |
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- #--with-plugin-auto-load always enable the plugin manager by default |
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- #--with-bundles build bundles in addition to dylibs on Mac OS X |
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- #--with-bin-release build executables suitable for public release |
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- # no dll and such |
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- #--with-64 compile to 64-bit code |
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- #--with-universal build universal binaries on Mac OS X |
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- #--with-universal=CPUs build universal binaries targeting the given CPUs |
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- #--without-exe do not build executables |
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- #--with-relative-runpath=P specify an executable-relative DLL search path |
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- #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH |
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- #--with-limited-linker don't attempt to build especially large projects |
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- #--with-extra-action= script to call after the configuration is complete |
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- #--with-autodep automatic generation of dependencies (GNU make) |
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- #--with-fake-root=DIR appear to have been built under DIR |
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- #--with-build-root-sfx=X add a user-specified suffix to the build dir name |
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- #--without-execopy do not copy built executables to the BIN area |
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- #--with-lib-rebuilds ensure that apps use up-to-date libraries |
187 |
- #--with-lib-rebuilds=ask ask whether to update each app's libraries |
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- #--without-deactivation keep old copies of libraries that no longer build |
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- #--without-makefile-auto-update do not auto-update generated makefiles |
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- #--with-projects=FILE build projects listed in FILE by default |
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- #--without-flat-makefile do not generate an all-encompassing flat makefile |
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- #--with-configure-dialog allow interactive flat makefile project selection |
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- #--with-saved-settings=F load configuration settings from the file F |
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- #--with-check-tools=... use the specified tools for testing |
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- #--with-ncbi-public ensure compatibility for all in-house platforms |
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- #--with-sybase-local=DIR use local SYBASE install (DIR is optional) |
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- #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) |
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- #--without-sp do not use SP libraries |
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- #--without-orbacus do not use ORBacus CORBA libraries |
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- #--with-orbacus=DIR use ORBacus installation in DIR |
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- #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) |
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- #--with-sablot=DIR use Sablotron installation in DIR |
203 |
- #--without-sablot, do not use Sablotron |
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- #--with-oechem=DIR use OpenEye OEChem installation in DIR |
205 |
- #--without-oechem do not use OEChem |
206 |
- #--with-sge=DIR use Sun Grid Engine installation in DIR |
207 |
- #--without-sge do not use Sun Grid Engine |
208 |
- #--with-magic=DIR use libmagic installation in DIR |
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- #--without-magic do not use libmagic |
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- #--without-local-lbsm turn off support for IPC with locally running LBSMD |
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- #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt |
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- #--without-connext do not build non-public CONNECT library extensions |
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- #--without-serial do not build the serialization library and tools |
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- #--without-objects do not generate/build serializeable objects from ASNs |
215 |
- #--without-dbapi do not build database connectivity libraries |
216 |
- #--without-app do not build standalone applications like ID1_FETCH |
217 |
- #--without-gui do not build most graphical projects |
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- #--without-algo do not build CPU-intensive algorithms |
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- #--without-internal do not build internal projects |
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- #--with-gbench ensure that Genome Workbench can be built |
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- #--without-gbench do not build Genome Workbench |
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- myconf+=( |
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- --with-dll |
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- --with-lfs |
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- --with-build-root="${S}"_build |
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- --without-suffix |
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- --without-hostspec |
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- --without-version |
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- --with-bincopy |
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- --without-strip |
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- --without-ccache |
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- --without-distcc |
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-# --with-ncbi-c |
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- --without-ctools |
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-# --with-sss |
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-# --with-sssutils |
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-# --with-sssdb |
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-# --with-included-sss |
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- --with-z="${EPREFIX}/usr" |
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- --with-bz2="${EPREFIX}/usr" |
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- --without-sybase |
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- --with-autodep |
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-# --with-3psw=std:netopt favor standard (system) builds of the above pkgs |
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- $(use_with debug) |
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- $(use_with debug max-debug) |
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- $(use_with debug symbols) |
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- $(use_with static-libs static) |
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- $(use_with static static-exe) |
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- $(use_with threads mt) |
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- $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") |
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- $(use_with test check) |
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- $(use_with pch) |
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- $(use_with lzo lzo "${EPREFIX}/usr") |
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- $(use_with pcre pcre "${EPREFIX}/usr") |
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- $(use_with gnutls gnutls "${EPREFIX}/usr") |
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- $(use_with mysql mysql "${EPREFIX}/usr") |
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- $(use_with muparser muparser "${EPREFIX}/usr") |
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- $(usex fltk --with-fltk="${EPREFIX}/usr" "") |
259 |
- $(use_with opengl opengl "${EPREFIX}/usr") |
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- $(use_with mesa mesa "${EPREFIX}/usr") |
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- $(use_with opengl glut "${EPREFIX}/usr") |
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- $(use_with opengl glew "${EPREFIX}/usr") |
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- $(use_with opengl glew-mx) |
264 |
- $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") |
265 |
- $(use_with wxwidgets wxwidgets-ucs) |
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- $(use_with freetype freetype "${EPREFIX}/usr") |
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-# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+ |
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- $(usex odbc --with-odbc="${EPREFIX}/usr" "") |
269 |
- $(use_with python python "${EPREFIX}/usr") |
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- $(use_with boost boost "${EPREFIX}/usr") |
271 |
- $(use_with sqlite sqlite3 "${EPREFIX}/usr") |
272 |
- $(use_with icu icu "${EPREFIX}/usr") |
273 |
- $(use_with expat expat "${EPREFIX}/usr") |
274 |
- $(use_with xml libxml "${EPREFIX}/usr") |
275 |
- $(use_with xml libxslt "${EPREFIX}/usr") |
276 |
- $(use_with xerces xerces "${EPREFIX}/usr") |
277 |
- $(use_with hdf5 hdf5 "${EPREFIX}/usr") |
278 |
- $(use_with xalan xalan "${EPREFIX}/usr") |
279 |
-# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" |
280 |
- --without-gif |
281 |
- $(use_with jpeg jpeg "${EPREFIX}/usr") |
282 |
- $(use_with tiff tiff "${EPREFIX}/usr") |
283 |
- $(use_with png png "${EPREFIX}/usr") |
284 |
- $(use_with xpm xpm "${EPREFIX}/usr") |
285 |
- $(use_with curl curl "${EPREFIX}/usr") |
286 |
-# $(use_with X x "${EPREFIX}/usr") |
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-# $(use_with X x) # there is no --with-x option |
288 |
- ) |
289 |
- |
290 |
- # http://www.ncbi.nlm.nih.gov/books/NBK7167/ |
291 |
- use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) |
292 |
- |
293 |
- # TODO |
294 |
- # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure |
295 |
- # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 |
296 |
- |
297 |
- einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" |
298 |
- |
299 |
-# ECONF_SOURCE="src/build-system" \ |
300 |
-# econf \ |
301 |
- bash \ |
302 |
- ./src/build-system/configure \ |
303 |
- --srcdir="${S}" \ |
304 |
- --prefix="${EPREFIX}/usr" \ |
305 |
- --libdir=/usr/lib64 \ |
306 |
- --with-flat-makefile \ |
307 |
- ${myconf[@]} || die "gcc 7 or newer were not used by upstream hence unsupported" |
308 |
-#--without-debug \ |
309 |
-# --with-bin-release \ |
310 |
-# --with-bincopy \ |
311 |
-# --without-static \ |
312 |
-# --with-dll \ |
313 |
-# --with-mt \ |
314 |
-# --with-openmp \ |
315 |
-# --with-lfs \ |
316 |
-# --prefix="${ED}"/usr \ |
317 |
-# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ |
318 |
-# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ |
319 |
-# || die |
320 |
-# econf ${myconf[@]} |
321 |
-} |
322 |
- |
323 |
-src_compile() { |
324 |
- ## all_r would ignore the --with-projects contents and build more |
325 |
- ## emake all_r -C GCC*-Release*/build || die |
326 |
- ## all_p with compile only selected/required components |
327 |
- ##cd "${S}"_build &&\ |
328 |
- ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" |
329 |
- #emake all_p -C "${S}"_build/build |
330 |
- |
331 |
- # |
332 |
- # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' |
333 |
- # |
334 |
- # The next release should automatically address such underlinking, albeit |
335 |
- # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to |
336 |
- # add or extend more DLL_LIB settings, to which end you may find the |
337 |
- # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ |
338 |
- # helpful. For instance, |
339 |
- # |
340 |
- # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html |
341 |
- # |
342 |
- # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set |
343 |
- # |
344 |
- # DLL_LIB = xncbi |
345 |
- # |
346 |
- # (You can find the path to that makefile by examining |
347 |
- # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) |
348 |
- # |
349 |
- # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: |
350 |
- emake -C "${S}"_build/build -f Makefile.flat |
351 |
-} |
352 |
- |
353 |
-src_install() { |
354 |
- rm -rvf "${S}"_build/lib/ncbi || die |
355 |
- emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" |
356 |
- |
357 |
-# dobin "${S}"_build/bin/* |
358 |
-# dolib.so "${S}"_build/lib/*so* |
359 |
-# dolib.a "${S}"_build/lib/*.a |
360 |
-# doheader "${S}"_build/inc/* |
361 |
- |
362 |
- # File collisions with sci-biology/ncbi-tools |
363 |
- mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ |
364 |
- mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ |
365 |
- mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries |
366 |
- mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ |
367 |
- mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ |
368 |
- |
369 |
- echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} |
370 |
- doenvd "${S}/99${PN}" |
371 |
-} |
372 |
- |
373 |
-pkg_postinst() { |
374 |
- einfo 'Please run "source /etc/profile" before using this package in the current shell.' |
375 |
- einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' |
376 |
-} |
377 |
|
378 |
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild |
379 |
deleted file mode 100644 |
380 |
index 0118086c8..000000000 |
381 |
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild |
382 |
+++ /dev/null |
383 |
@@ -1,355 +0,0 @@ |
384 |
-# Copyright 1999-2021 Gentoo Authors |
385 |
-# Distributed under the terms of the GNU General Public License v2 |
386 |
- |
387 |
-EAPI=7 |
388 |
- |
389 |
-PYTHON_COMPAT=( python2_7 ) |
390 |
- |
391 |
-inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs |
392 |
- |
393 |
-MY_P="ncbi-blast-${PV}+-src" |
394 |
-# workdir/ncbi-blast-2.2.30+-src |
395 |
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz |
396 |
- |
397 |
-DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+" |
398 |
-HOMEPAGE="https://ncbi.github.io/cxx-toolkit/t" |
399 |
-SRC_URI=" |
400 |
- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz" |
401 |
-# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" |
402 |
- |
403 |
-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz |
404 |
-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html |
405 |
-LICENSE="public-domain" |
406 |
-SLOT="0" |
407 |
-IUSE=" |
408 |
- debug static-libs static threads pch |
409 |
- test wxwidgets odbc |
410 |
- berkdb boost bzip2 cppunit curl expat fltk freetype gif |
411 |
- glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python |
412 |
- sablotron sqlite tiff xerces xalan xml xpm xslt X" |
413 |
-KEYWORDS="~amd64 ~x86" |
414 |
-RESTRICT="!test? ( test )" |
415 |
- |
416 |
-REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
417 |
- |
418 |
-# sys-libs/db should be compiled with USE=cxx |
419 |
-DEPEND=" |
420 |
- <sys-devel/gcc-10:= |
421 |
- !sci-biology/ncbi-tools++ |
422 |
- !sci-biology/sra_sdk |
423 |
- berkdb? ( sys-libs/db:4.3[cxx] ) |
424 |
- boost? ( dev-libs/boost ) |
425 |
- curl? ( net-misc/curl ) |
426 |
- sqlite? ( dev-db/sqlite:3 ) |
427 |
- mysql? ( virtual/mysql ) |
428 |
- fltk? ( x11-libs/fltk ) |
429 |
- opengl? ( virtual/opengl media-libs/glew:0= ) |
430 |
- mesa? ( media-libs/mesa[osmesa] ) |
431 |
- glut? ( media-libs/freeglut ) |
432 |
- freetype? ( media-libs/freetype ) |
433 |
- gnutls? ( net-libs/gnutls ) |
434 |
- python? ( ${PYTHON_DEPS} ) |
435 |
- cppunit? ( dev-util/cppunit ) |
436 |
- icu? ( dev-libs/icu ) |
437 |
- expat? ( dev-libs/expat ) |
438 |
- sablotron? ( app-text/sablotron ) |
439 |
- xml? ( dev-libs/libxml2 ) |
440 |
- xslt? ( dev-libs/libxslt ) |
441 |
- xerces? ( dev-libs/xerces-c ) |
442 |
- xalan? ( dev-libs/xalan-c ) |
443 |
- muparser? ( dev-cpp/muParser ) |
444 |
- hdf5? ( sci-libs/hdf5[cxx] ) |
445 |
- gif? ( media-libs/giflib ) |
446 |
- jpeg? ( virtual/jpeg:0= ) |
447 |
- png? ( media-libs/libpng:0= ) |
448 |
- tiff? ( media-libs/tiff:0= ) |
449 |
- xpm? ( x11-libs/libXpm ) |
450 |
- dev-libs/lzo |
451 |
- app-arch/bzip2 |
452 |
- dev-libs/libpcre" |
453 |
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge |
454 |
-# Intentionally omitted USE flags: |
455 |
-# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. |
456 |
-# The default (heavily patched) embedded copy should work, or you can |
457 |
-# leave it off altogether -- the only public apps that make use of it are |
458 |
-# samples and tests, since NCBI's database servers are of course firewalled. |
459 |
- |
460 |
-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) |
461 |
- |
462 |
-RDEPEND="${DEPEND}" |
463 |
- |
464 |
-S="${WORKDIR}/${MY_P}/c++" |
465 |
-# ncbi-blast-2.2.30+-src/c++ |
466 |
- |
467 |
-src_prepare() { |
468 |
-# filter-ldflags -Wl,--as-needed |
469 |
-# append-ldflags -Wl,--no-undefined |
470 |
-# sed -i -e 's/-print-file-name=libstdc++.a//' \ |
471 |
-# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ |
472 |
-# src/build-system/configure || die |
473 |
-# epatch \ |
474 |
-# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ |
475 |
-# "${FILESDIR}"/curl-types.patch \ |
476 |
-# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ |
477 |
-# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ |
478 |
-# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ |
479 |
-# "${FILESDIR}"/report_project_settings_configure.ac.patch \ |
480 |
-# "${FILESDIR}"/report_project_settings_configure.patch \ |
481 |
-# "${FILESDIR}"/make_install.patch |
482 |
- |
483 |
-# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch |
484 |
- |
485 |
-# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ |
486 |
-# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ |
487 |
-# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ |
488 |
-# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ |
489 |
-# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch |
490 |
- |
491 |
-# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" |
492 |
- |
493 |
-# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers |
494 |
-## local PATCHES=( |
495 |
-## "${FILESDIR}"/${P}-conf-opts.patch |
496 |
-## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch |
497 |
-## "${FILESDIR}"/${P}-linkage-tuneups.patch |
498 |
-## "${FILESDIR}"/${P}-more-patches.patch |
499 |
-## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch |
500 |
-## "${FILESDIR}"/${P}-configure.patch |
501 |
-## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch |
502 |
-## "${FILESDIR}"/${P}-fix-install.patch |
503 |
-## ) |
504 |
- # "${FILESDIR}"/${P}-support-autoconf-2.60.patch |
505 |
-## epatch ${PATCHES[@]} |
506 |
- |
507 |
- # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup |
508 |
- # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere |
509 |
- # it is still present, plus in a few places was something else patched |
510 |
- # staying without any patches for now and lets see is it works on Gentoo |
511 |
- # epatch "${FILESDIR}"/fix_lib_deps.patch |
512 |
- # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 |
513 |
- # https://bugs.gentoo.org/show_bug.cgi?id=514706 |
514 |
- |
515 |
- tc-export CXX CC |
516 |
- |
517 |
-## cd src/build-system || die |
518 |
-# eautoreconf |
519 |
- |
520 |
- # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch |
521 |
- # eautoconf # keep it disabled until we can ensure 2.59 is installed |
522 |
- # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support |
523 |
- default |
524 |
-} |
525 |
- |
526 |
-# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site |
527 |
-src_configure() { |
528 |
- local myconf=() |
529 |
- #--without-optimization turn off optimization flags in non-debug mode |
530 |
- #--with-profiling build profiled versions of libs and apps |
531 |
- #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) |
532 |
- #--with-plugin-auto-load always enable the plugin manager by default |
533 |
- #--with-bundles build bundles in addition to dylibs on Mac OS X |
534 |
- #--with-bin-release build executables suitable for public release |
535 |
- # no dll and such |
536 |
- #--with-64 compile to 64-bit code |
537 |
- #--with-universal build universal binaries on Mac OS X |
538 |
- #--with-universal=CPUs build universal binaries targeting the given CPUs |
539 |
- #--without-exe do not build executables |
540 |
- #--with-relative-runpath=P specify an executable-relative DLL search path |
541 |
- #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH |
542 |
- #--with-limited-linker don't attempt to build especially large projects |
543 |
- #--with-extra-action= script to call after the configuration is complete |
544 |
- #--with-autodep automatic generation of dependencies (GNU make) |
545 |
- #--with-fake-root=DIR appear to have been built under DIR |
546 |
- #--with-build-root-sfx=X add a user-specified suffix to the build dir name |
547 |
- #--without-execopy do not copy built executables to the BIN area |
548 |
- #--with-lib-rebuilds ensure that apps use up-to-date libraries |
549 |
- #--with-lib-rebuilds=ask ask whether to update each app's libraries |
550 |
- #--without-deactivation keep old copies of libraries that no longer build |
551 |
- #--without-makefile-auto-update do not auto-update generated makefiles |
552 |
- #--with-projects=FILE build projects listed in FILE by default |
553 |
- #--without-flat-makefile do not generate an all-encompassing flat makefile |
554 |
- #--with-configure-dialog allow interactive flat makefile project selection |
555 |
- #--with-saved-settings=F load configuration settings from the file F |
556 |
- #--with-check-tools=... use the specified tools for testing |
557 |
- #--with-ncbi-public ensure compatibility for all in-house platforms |
558 |
- #--with-sybase-local=DIR use local SYBASE install (DIR is optional) |
559 |
- #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) |
560 |
- #--without-sp do not use SP libraries |
561 |
- #--without-orbacus do not use ORBacus CORBA libraries |
562 |
- #--with-orbacus=DIR use ORBacus installation in DIR |
563 |
- #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) |
564 |
- #--with-sablot=DIR use Sablotron installation in DIR |
565 |
- #--without-sablot, do not use Sablotron |
566 |
- #--with-oechem=DIR use OpenEye OEChem installation in DIR |
567 |
- #--without-oechem do not use OEChem |
568 |
- #--with-sge=DIR use Sun Grid Engine installation in DIR |
569 |
- #--without-sge do not use Sun Grid Engine |
570 |
- #--with-magic=DIR use libmagic installation in DIR |
571 |
- #--without-magic do not use libmagic |
572 |
- #--without-local-lbsm turn off support for IPC with locally running LBSMD |
573 |
- #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt |
574 |
- #--without-connext do not build non-public CONNECT library extensions |
575 |
- #--without-serial do not build the serialization library and tools |
576 |
- #--without-objects do not generate/build serializeable objects from ASNs |
577 |
- #--without-dbapi do not build database connectivity libraries |
578 |
- #--without-app do not build standalone applications like ID1_FETCH |
579 |
- #--without-gui do not build most graphical projects |
580 |
- #--without-algo do not build CPU-intensive algorithms |
581 |
- #--without-internal do not build internal projects |
582 |
- #--with-gbench ensure that Genome Workbench can be built |
583 |
- #--without-gbench do not build Genome Workbench |
584 |
- myconf+=( |
585 |
- --with-dll |
586 |
- --with-lfs |
587 |
- --with-build-root="${S}"_build |
588 |
- --without-suffix |
589 |
- --without-hostspec |
590 |
- --without-version |
591 |
- --with-bincopy |
592 |
- --without-strip |
593 |
- --without-ccache |
594 |
- --without-distcc |
595 |
-# --with-ncbi-c |
596 |
- --without-ctools |
597 |
-# --with-sss |
598 |
-# --with-sssutils |
599 |
-# --with-sssdb |
600 |
-# --with-included-sss |
601 |
- --with-z="${EPREFIX}/usr" |
602 |
- --with-bz2="${EPREFIX}/usr" |
603 |
- --without-sybase |
604 |
- --with-autodep |
605 |
-# --with-3psw=std:netopt favor standard (system) builds of the above pkgs |
606 |
- $(use_with debug) |
607 |
- $(use_with debug max-debug) |
608 |
- $(use_with debug symbols) |
609 |
- $(use_with static-libs static) |
610 |
- $(use_with static static-exe) |
611 |
- $(use_with threads mt) |
612 |
- $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") |
613 |
- $(use_with test check) |
614 |
- $(use_with pch) |
615 |
- $(use_with lzo lzo "${EPREFIX}/usr") |
616 |
- $(use_with pcre pcre "${EPREFIX}/usr") |
617 |
- $(use_with gnutls gnutls "${EPREFIX}/usr") |
618 |
- $(use_with mysql mysql "${EPREFIX}/usr") |
619 |
- $(use_with muparser muparser "${EPREFIX}/usr") |
620 |
- $(usex fltk --with-fltk="${EPREFIX}/usr" "") |
621 |
- $(use_with opengl opengl "${EPREFIX}/usr") |
622 |
- $(use_with mesa mesa "${EPREFIX}/usr") |
623 |
- $(use_with opengl glut "${EPREFIX}/usr") |
624 |
- $(use_with opengl glew "${EPREFIX}/usr") |
625 |
- $(use_with opengl glew-mx) |
626 |
- $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") |
627 |
- $(use_with wxwidgets wxwidgets-ucs) |
628 |
- $(use_with freetype freetype "${EPREFIX}/usr") |
629 |
-# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+ |
630 |
- $(usex odbc --with-odbc="${EPREFIX}/usr" "") |
631 |
- $(use_with python python "${EPREFIX}/usr") |
632 |
- $(use_with boost boost "${EPREFIX}/usr") |
633 |
- $(use_with sqlite sqlite3 "${EPREFIX}/usr") |
634 |
- $(use_with icu icu "${EPREFIX}/usr") |
635 |
- $(use_with expat expat "${EPREFIX}/usr") |
636 |
- $(use_with xml libxml "${EPREFIX}/usr") |
637 |
- $(use_with xml libxslt "${EPREFIX}/usr") |
638 |
- $(use_with xerces xerces "${EPREFIX}/usr") |
639 |
- $(use_with hdf5 hdf5 "${EPREFIX}/usr") |
640 |
- $(use_with xalan xalan "${EPREFIX}/usr") |
641 |
-# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" |
642 |
- --without-gif |
643 |
- $(use_with jpeg jpeg "${EPREFIX}/usr") |
644 |
- $(use_with tiff tiff "${EPREFIX}/usr") |
645 |
- $(use_with png png "${EPREFIX}/usr") |
646 |
- $(use_with xpm xpm "${EPREFIX}/usr") |
647 |
- $(use_with curl curl "${EPREFIX}/usr") |
648 |
-# $(use_with X x "${EPREFIX}/usr") |
649 |
-# $(use_with X x) # there is no --with-x option |
650 |
- ) |
651 |
- |
652 |
- # http://www.ncbi.nlm.nih.gov/books/NBK7167/ |
653 |
- use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) |
654 |
- |
655 |
- # TODO |
656 |
- # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure |
657 |
- # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 |
658 |
- |
659 |
- einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" |
660 |
- |
661 |
-# ECONF_SOURCE="src/build-system" \ |
662 |
-# econf \ |
663 |
- bash \ |
664 |
- ./src/build-system/configure \ |
665 |
- --srcdir="${S}" \ |
666 |
- --prefix="${EPREFIX}/usr" \ |
667 |
- --libdir=/usr/lib64 \ |
668 |
- --with-flat-makefile \ |
669 |
- ${myconf[@]} || die "gcc 7 or newer were not used by upstream hence unsupported" |
670 |
-#--without-debug \ |
671 |
-# --with-bin-release \ |
672 |
-# --with-bincopy \ |
673 |
-# --without-static \ |
674 |
-# --with-dll \ |
675 |
-# --with-mt \ |
676 |
-# --with-openmp \ |
677 |
-# --with-lfs \ |
678 |
-# --prefix="${ED}"/usr \ |
679 |
-# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ |
680 |
-# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ |
681 |
-# || die |
682 |
-# econf ${myconf[@]} |
683 |
-} |
684 |
- |
685 |
-src_compile() { |
686 |
- ## all_r would ignore the --with-projects contents and build more |
687 |
- ## emake all_r -C GCC*-Release*/build || die |
688 |
- ## all_p with compile only selected/required components |
689 |
- ##cd "${S}"_build &&\ |
690 |
- ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" |
691 |
- #emake all_p -C "${S}"_build/build |
692 |
- |
693 |
- # |
694 |
- # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' |
695 |
- # |
696 |
- # The next release should automatically address such underlinking, albeit |
697 |
- # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to |
698 |
- # add or extend more DLL_LIB settings, to which end you may find the |
699 |
- # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ |
700 |
- # helpful. For instance, |
701 |
- # |
702 |
- # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html |
703 |
- # |
704 |
- # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set |
705 |
- # |
706 |
- # DLL_LIB = xncbi |
707 |
- # |
708 |
- # (You can find the path to that makefile by examining |
709 |
- # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) |
710 |
- # |
711 |
- # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: |
712 |
- emake -C "${S}"_build/build -f Makefile.flat |
713 |
-} |
714 |
- |
715 |
-src_install() { |
716 |
- rm -rvf "${S}"_build/lib/ncbi || die |
717 |
- emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" |
718 |
- |
719 |
-# dobin "${S}"_build/bin/* |
720 |
-# dolib.so "${S}"_build/lib/*so* |
721 |
-# dolib.a "${S}"_build/lib/*.a |
722 |
-# doheader "${S}"_build/inc/* |
723 |
- |
724 |
- # File collisions with sci-biology/ncbi-tools |
725 |
- mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ |
726 |
- mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ |
727 |
- mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries |
728 |
- mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ |
729 |
- mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ |
730 |
- |
731 |
- echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} |
732 |
- doenvd "${S}/99${PN}" |
733 |
-} |
734 |
- |
735 |
-pkg_postinst() { |
736 |
- einfo 'Please run "source /etc/profile" before using this package in the current shell.' |
737 |
- einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' |
738 |
-} |
739 |
|
740 |
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild |
741 |
deleted file mode 100644 |
742 |
index ccedf666d..000000000 |
743 |
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild |
744 |
+++ /dev/null |
745 |
@@ -1,360 +0,0 @@ |
746 |
-# Copyright 1999-2021 Gentoo Authors |
747 |
-# Distributed under the terms of the GNU General Public License v2 |
748 |
- |
749 |
-EAPI=7 |
750 |
- |
751 |
-PYTHON_COMPAT=( python2_7 ) |
752 |
- |
753 |
-inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs |
754 |
- |
755 |
-MY_P="ncbi-blast-${PV}+-src" |
756 |
-# workdir/ncbi-blast-2.2.30+-src |
757 |
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz |
758 |
-# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz |
759 |
- |
760 |
-DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+" |
761 |
-HOMEPAGE="https://ncbi.github.io/cxx-toolkit/" |
762 |
-SRC_URI=" |
763 |
- ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz" |
764 |
-# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" |
765 |
- |
766 |
-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz |
767 |
-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html |
768 |
-LICENSE="public-domain" |
769 |
-SLOT="0" |
770 |
-IUSE=" |
771 |
- debug static-libs static threads pch |
772 |
- test wxwidgets odbc |
773 |
- berkdb boost bzip2 cppunit curl expat fltk freetype gif |
774 |
- glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python |
775 |
- sablotron sqlite tiff xerces xalan xml xpm xslt X" |
776 |
-KEYWORDS="~amd64 ~x86" |
777 |
-RESTRICT="!test? ( test )" |
778 |
- |
779 |
-REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
780 |
- |
781 |
-# sys-libs/db should be compiled with USE=cxx |
782 |
-DEPEND=" |
783 |
- <sys-devel/gcc-10:= |
784 |
- !sci-biology/ncbi-tools++ |
785 |
- !sci-biology/sra_sdk |
786 |
- berkdb? ( sys-libs/db:4.3[cxx] ) |
787 |
- boost? ( dev-libs/boost ) |
788 |
- curl? ( net-misc/curl ) |
789 |
- sqlite? ( dev-db/sqlite:3 ) |
790 |
- mysql? ( virtual/mysql ) |
791 |
- fltk? ( x11-libs/fltk ) |
792 |
- opengl? ( virtual/opengl media-libs/glew:0= ) |
793 |
- mesa? ( media-libs/mesa[osmesa] ) |
794 |
- glut? ( media-libs/freeglut ) |
795 |
- freetype? ( media-libs/freetype ) |
796 |
- gnutls? ( net-libs/gnutls ) |
797 |
- python? ( ${PYTHON_DEPS} ) |
798 |
- cppunit? ( dev-util/cppunit ) |
799 |
- icu? ( dev-libs/icu ) |
800 |
- expat? ( dev-libs/expat ) |
801 |
- sablotron? ( app-text/sablotron ) |
802 |
- xml? ( dev-libs/libxml2 ) |
803 |
- xslt? ( dev-libs/libxslt ) |
804 |
- xerces? ( dev-libs/xerces-c ) |
805 |
- xalan? ( dev-libs/xalan-c ) |
806 |
- muparser? ( dev-cpp/muParser ) |
807 |
- hdf5? ( sci-libs/hdf5[cxx] ) |
808 |
- gif? ( media-libs/giflib ) |
809 |
- jpeg? ( virtual/jpeg:0= ) |
810 |
- png? ( media-libs/libpng:0= ) |
811 |
- tiff? ( media-libs/tiff:0= ) |
812 |
- xpm? ( x11-libs/libXpm ) |
813 |
- dev-libs/lzo |
814 |
- app-arch/bzip2 |
815 |
- dev-libs/libpcre" |
816 |
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge |
817 |
-# Intentionally omitted USE flags: |
818 |
-# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. |
819 |
-# The default (heavily patched) embedded copy should work, or you can |
820 |
-# leave it off altogether -- the only public apps that make use of it are |
821 |
-# samples and tests, since NCBI's database servers are of course firewalled. |
822 |
- |
823 |
-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) |
824 |
- |
825 |
-RDEPEND="${DEPEND}" |
826 |
- |
827 |
-S="${WORKDIR}/${MY_P}/c++" |
828 |
-# ncbi-blast-2.2.30+-src/c++ |
829 |
- |
830 |
-src_prepare() { |
831 |
-# filter-ldflags -Wl,--as-needed |
832 |
-# append-ldflags -Wl,--no-undefined |
833 |
-# sed -i -e 's/-print-file-name=libstdc++.a//' \ |
834 |
-# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ |
835 |
-# src/build-system/configure || die |
836 |
-# epatch \ |
837 |
-# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ |
838 |
-# "${FILESDIR}"/curl-types.patch \ |
839 |
-# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ |
840 |
-# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ |
841 |
-# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ |
842 |
-# "${FILESDIR}"/report_project_settings_configure.ac.patch \ |
843 |
-# "${FILESDIR}"/report_project_settings_configure.patch \ |
844 |
-# "${FILESDIR}"/make_install.patch |
845 |
- |
846 |
-# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch |
847 |
- |
848 |
-# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ |
849 |
-# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ |
850 |
-# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ |
851 |
-# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ |
852 |
-# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch |
853 |
- |
854 |
-# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" |
855 |
- |
856 |
-# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers |
857 |
-## local PATCHES=( |
858 |
-## "${FILESDIR}"/${P}-conf-opts.patch |
859 |
-## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch |
860 |
-## "${FILESDIR}"/${P}-linkage-tuneups.patch |
861 |
-## "${FILESDIR}"/${P}-more-patches.patch |
862 |
-## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch |
863 |
-## "${FILESDIR}"/${P}-configure.patch |
864 |
-## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch |
865 |
-## "${FILESDIR}"/${P}-fix-install.patch |
866 |
-## ) |
867 |
- # "${FILESDIR}"/${P}-support-autoconf-2.60.patch |
868 |
-## epatch ${PATCHES[@]} |
869 |
- |
870 |
- # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup |
871 |
- # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere |
872 |
- # it is still present, plus in a few places was something else patched |
873 |
- # staying without any patches for now and lets see is it works on Gentoo |
874 |
- # epatch "${FILESDIR}"/fix_lib_deps.patch |
875 |
- # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 |
876 |
- # https://bugs.gentoo.org/show_bug.cgi?id=514706 |
877 |
- |
878 |
- tc-export CXX CC |
879 |
- |
880 |
-## cd src/build-system || die |
881 |
-# eautoreconf |
882 |
- |
883 |
- # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch |
884 |
- # eautoconf # keep it disabled until we can ensure 2.59 is installed |
885 |
- # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support |
886 |
- default |
887 |
-} |
888 |
- |
889 |
-# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site |
890 |
-src_configure() { |
891 |
- local myconf=() |
892 |
- #--without-optimization turn off optimization flags in non-debug mode |
893 |
- #--with-profiling build profiled versions of libs and apps |
894 |
- #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) |
895 |
- #--with-plugin-auto-load always enable the plugin manager by default |
896 |
- #--with-bundles build bundles in addition to dylibs on Mac OS X |
897 |
- #--with-bin-release build executables suitable for public release |
898 |
- # no dll and such |
899 |
- #--with-64 compile to 64-bit code |
900 |
- #--with-universal build universal binaries on Mac OS X |
901 |
- #--with-universal=CPUs build universal binaries targeting the given CPUs |
902 |
- #--without-exe do not build executables |
903 |
- #--with-relative-runpath=P specify an executable-relative DLL search path |
904 |
- #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH |
905 |
- #--with-limited-linker don't attempt to build especially large projects |
906 |
- #--with-extra-action= script to call after the configuration is complete |
907 |
- #--with-autodep automatic generation of dependencies (GNU make) |
908 |
- #--with-fake-root=DIR appear to have been built under DIR |
909 |
- #--with-build-root-sfx=X add a user-specified suffix to the build dir name |
910 |
- #--without-execopy do not copy built executables to the BIN area |
911 |
- #--with-lib-rebuilds ensure that apps use up-to-date libraries |
912 |
- #--with-lib-rebuilds=ask ask whether to update each app's libraries |
913 |
- #--without-deactivation keep old copies of libraries that no longer build |
914 |
- #--without-makefile-auto-update do not auto-update generated makefiles |
915 |
- #--with-projects=FILE build projects listed in FILE by default |
916 |
- #--without-flat-makefile do not generate an all-encompassing flat makefile |
917 |
- #--with-configure-dialog allow interactive flat makefile project selection |
918 |
- #--with-saved-settings=F load configuration settings from the file F |
919 |
- #--with-check-tools=... use the specified tools for testing |
920 |
- #--with-ncbi-public ensure compatibility for all in-house platforms |
921 |
- #--with-sybase-local=DIR use local SYBASE install (DIR is optional) |
922 |
- #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) |
923 |
- #--without-sp do not use SP libraries |
924 |
- #--without-orbacus do not use ORBacus CORBA libraries |
925 |
- #--with-orbacus=DIR use ORBacus installation in DIR |
926 |
- #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) |
927 |
- #--with-sablot=DIR use Sablotron installation in DIR |
928 |
- #--without-sablot, do not use Sablotron |
929 |
- #--with-oechem=DIR use OpenEye OEChem installation in DIR |
930 |
- #--without-oechem do not use OEChem |
931 |
- #--with-sge=DIR use Sun Grid Engine installation in DIR |
932 |
- #--without-sge do not use Sun Grid Engine |
933 |
- #--with-magic=DIR use libmagic installation in DIR |
934 |
- #--without-magic do not use libmagic |
935 |
- #--without-local-lbsm turn off support for IPC with locally running LBSMD |
936 |
- #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt |
937 |
- #--without-connext do not build non-public CONNECT library extensions |
938 |
- #--without-serial do not build the serialization library and tools |
939 |
- #--without-objects do not generate/build serializeable objects from ASNs |
940 |
- #--without-dbapi do not build database connectivity libraries |
941 |
- #--without-app do not build standalone applications like ID1_FETCH |
942 |
- #--without-gui do not build most graphical projects |
943 |
- #--without-algo do not build CPU-intensive algorithms |
944 |
- #--without-internal do not build internal projects |
945 |
- #--with-gbench ensure that Genome Workbench can be built |
946 |
- #--without-gbench do not build Genome Workbench |
947 |
- myconf+=( |
948 |
- --with-dll |
949 |
- --with-lfs |
950 |
- --with-build-root="${S}"_build |
951 |
- --without-suffix |
952 |
- --without-hostspec |
953 |
- --without-version |
954 |
- --with-bincopy |
955 |
- --without-strip |
956 |
- --without-ccache |
957 |
- --without-distcc |
958 |
-# --with-ncbi-c |
959 |
- --without-ctools |
960 |
-# --with-sss |
961 |
-# --with-sssutils |
962 |
-# --with-sssdb |
963 |
-# --with-included-sss |
964 |
- --with-z="${EPREFIX}/usr" |
965 |
- --with-bz2="${EPREFIX}/usr" |
966 |
- --without-sybase |
967 |
- --with-autodep |
968 |
-# --with-3psw=std:netopt favor standard (system) builds of the above pkgs |
969 |
- $(use_with debug) |
970 |
- $(use_with debug max-debug) |
971 |
- $(use_with debug symbols) |
972 |
- $(use_with static-libs static) |
973 |
- $(use_with static static-exe) |
974 |
- $(use_with threads mt) |
975 |
- $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") |
976 |
- $(use_with test check) |
977 |
- $(use_with pch) |
978 |
- $(use_with lzo lzo "${EPREFIX}/usr") |
979 |
- $(use_with pcre pcre "${EPREFIX}/usr") |
980 |
- $(use_with gnutls gnutls "${EPREFIX}/usr") |
981 |
- $(use_with mysql mysql "${EPREFIX}/usr") |
982 |
- $(use_with muparser muparser "${EPREFIX}/usr") |
983 |
- $(usex fltk --with-fltk="${EPREFIX}/usr" "") |
984 |
- $(use_with opengl opengl "${EPREFIX}/usr") |
985 |
- $(use_with mesa mesa "${EPREFIX}/usr") |
986 |
- $(use_with opengl glut "${EPREFIX}/usr") |
987 |
- $(use_with opengl glew "${EPREFIX}/usr") |
988 |
- # |
989 |
- # GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302 |
990 |
- # $(use_with opengl glew-mx) |
991 |
- $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") |
992 |
- $(use_with wxwidgets wxwidgets-ucs) |
993 |
- $(use_with freetype freetype "${EPREFIX}/usr") |
994 |
-# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+ |
995 |
- $(usex odbc --with-odbc="${EPREFIX}/usr" "") |
996 |
- $(use_with python python "${EPREFIX}/usr") |
997 |
- $(use_with boost boost "${EPREFIX}/usr") |
998 |
- $(use_with sqlite sqlite3 "${EPREFIX}/usr") |
999 |
- $(use_with icu icu "${EPREFIX}/usr") |
1000 |
- $(use_with expat expat "${EPREFIX}/usr") |
1001 |
- $(use_with xml libxml "${EPREFIX}/usr") |
1002 |
- $(use_with xml libxslt "${EPREFIX}/usr") |
1003 |
- $(use_with xerces xerces "${EPREFIX}/usr") |
1004 |
- $(use_with hdf5 hdf5 "${EPREFIX}/usr") |
1005 |
- $(use_with xalan xalan "${EPREFIX}/usr") |
1006 |
-# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" |
1007 |
- --without-gif |
1008 |
- $(use_with jpeg jpeg "${EPREFIX}/usr") |
1009 |
- $(use_with tiff tiff "${EPREFIX}/usr") |
1010 |
- $(use_with png png "${EPREFIX}/usr") |
1011 |
- $(use_with xpm xpm "${EPREFIX}/usr") |
1012 |
- $(use_with curl curl "${EPREFIX}/usr") |
1013 |
-# $(use_with X x "${EPREFIX}/usr") |
1014 |
-# $(use_with X x) # there is no --with-x option |
1015 |
- # prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution |
1016 |
- --without-vdb |
1017 |
- ) |
1018 |
- |
1019 |
- # http://www.ncbi.nlm.nih.gov/books/NBK7167/ |
1020 |
- use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) |
1021 |
- |
1022 |
- # TODO |
1023 |
- # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure |
1024 |
- # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 |
1025 |
- |
1026 |
- einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" |
1027 |
- |
1028 |
-# ECONF_SOURCE="src/build-system" \ |
1029 |
-# econf \ |
1030 |
- bash \ |
1031 |
- ./src/build-system/configure \ |
1032 |
- --srcdir="${S}" \ |
1033 |
- --prefix="${EPREFIX}/usr" \ |
1034 |
- --libdir=/usr/lib64 \ |
1035 |
- --with-flat-makefile \ |
1036 |
- ${myconf[@]} || die |
1037 |
-#--without-debug \ |
1038 |
-# --with-bin-release \ |
1039 |
-# --with-bincopy \ |
1040 |
-# --without-static \ |
1041 |
-# --with-dll \ |
1042 |
-# --with-mt \ |
1043 |
-# --with-openmp \ |
1044 |
-# --with-lfs \ |
1045 |
-# --prefix="${ED}"/usr \ |
1046 |
-# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ |
1047 |
-# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ |
1048 |
-# || die |
1049 |
-# econf ${myconf[@]} |
1050 |
-} |
1051 |
- |
1052 |
-src_compile() { |
1053 |
- ## all_r would ignore the --with-projects contents and build more |
1054 |
- ## emake all_r -C GCC*-Release*/build || die |
1055 |
- ## all_p with compile only selected/required components |
1056 |
- ##cd "${S}"_build &&\ |
1057 |
- ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" |
1058 |
- #emake all_p -C "${S}"_build/build |
1059 |
- |
1060 |
- # |
1061 |
- # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' |
1062 |
- # |
1063 |
- # The next release should automatically address such underlinking, albeit |
1064 |
- # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to |
1065 |
- # add or extend more DLL_LIB settings, to which end you may find the |
1066 |
- # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ |
1067 |
- # helpful. For instance, |
1068 |
- # |
1069 |
- # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html |
1070 |
- # |
1071 |
- # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set |
1072 |
- # |
1073 |
- # DLL_LIB = xncbi |
1074 |
- # |
1075 |
- # (You can find the path to that makefile by examining |
1076 |
- # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) |
1077 |
- # |
1078 |
- # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: |
1079 |
- emake -C "${S}"_build/build -f Makefile.flat |
1080 |
-} |
1081 |
- |
1082 |
-src_install() { |
1083 |
- rm -rvf "${S}"_build/lib/ncbi || die |
1084 |
- emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" |
1085 |
- |
1086 |
-# dobin "${S}"_build/bin/* |
1087 |
-# dolib.so "${S}"_build/lib/*so* |
1088 |
-# dolib.a "${S}"_build/lib/*.a |
1089 |
-# doheader "${S}"_build/inc/* |
1090 |
- |
1091 |
- # File collisions with sci-biology/ncbi-tools |
1092 |
- mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ |
1093 |
- mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ |
1094 |
- mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries |
1095 |
- mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ |
1096 |
- mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ |
1097 |
- |
1098 |
- echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} |
1099 |
- doenvd "${S}/99${PN}" |
1100 |
-} |
1101 |
- |
1102 |
-pkg_postinst() { |
1103 |
- einfo 'Please run "source /etc/profile" before using this package in the current shell.' |
1104 |
- einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' |
1105 |
-} |
1106 |
|
1107 |
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild |
1108 |
index 72f8fd0b1..40f338bc3 100644 |
1109 |
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild |
1110 |
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild |
1111 |
@@ -3,7 +3,7 @@ |
1112 |
|
1113 |
EAPI=7 |
1114 |
|
1115 |
-PYTHON_COMPAT=( python2_7 ) |
1116 |
+PYTHON_COMPAT=( python3_{7,8,9} ) |
1117 |
|
1118 |
inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs |